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2,481 results for “zebrafish”
Atomic force microscopy indentation data of zebrafish spinal cord sections
<p>The HDF5 file was created using the Python package nanite. It contains 1132 raw atomic force microscopy (AFM) force-indentation curves of zebrafish spinal cord sections, the preprocessed curves, and the corresponding fits to the approach part. In addition, a manual rating was assigned to each force-indentation curve. The intended use of this dataset is the application of machine-learning approaches to quantify AFM data quality for biological tissues.</p>
CompTox Zebrafish developmental toxicity processed data
<p>Please cite the published paper and original data source.</p> <p>A classification data set for 19 endpoints of Zebrafish developmental toxicity for QSAR modelling.</p> <p>The original data was downloaded from <a href="https://comptox.epa.gov/dashboard">https://comptox.epa.gov/dashboard</a></p> <p>See also references below.</p> <ul> <li>20201230_tx_zf.csv -- Endpoint data</li> <li>20201230_tx_zf_smiles.txt -- SMILES of the structures</li> <li>20201230_tx_zf_descriptors_rdkit.csv -- Descriptors</li> <li>20201230_tx_zf_fp_r3_v5120.csv -- Fingerprints</li> </ul>
Zebrafish Pathway Metabolite MetFrag Local CSV
<p>This is a local CSV file of Zebrafish metabolites for MetFrag (https://msbi.ipb-halle.de/MetFrag/) extracted from PubChem, based partially on previous data extracted from Wikipathways, KEGG and literature (DOI: <a href="https://doi.org/10.1371/journal.pone.0213661">10.1371/journal.pone.0213661</a>), combined in previous versions of this record (DOI: <a href="https://doi.org/10.5281/zenodo.3541624">10.5281/zenodo.3541624</a>).</p> <p>This file was created as documented on the <a href="https://gitlab.com/uniluxembourg/lcsb/eci/pubchem-docs/-/tree/main/taxonomy/Danio_rerio">ECI GitLab</a>. </p> <p>This file is designed for identification using MetFrag CL workflows (offline), this file will be integrated into MetFrag online; please use the file in the dropdown menu rather than uploading this one.</p> <p> </p>
Fluorescently-labelled zebrafish pronephroi + ground truth classes (normal/cystic) + trained CNN model
<p>This upload contains :</p> <p>- <strong>images.zip: </strong> microscope images of fluorescently-labelled pronephroi in larvae of the <em>Tg(wt1b:EGFP)</em> transgenic zebrafish line showing 2 morphologies (normal vs cystic) upon injection with Co-Mo or ift172-MO, respectively. Images were obtained using an ACQUIFER Imaging Machine widefield high content screening microscope.</p> <p>Reference: </p> <p>Pandey, G., Westhoff, J., Schaefer, F. and Gehrig, J. (2019). <strong>A Smart Imaging Workflow for Organ-Specific Screening in a Cystic Kidney Zebrafish Disease Model</strong>. International Journal of Molecular Sciences <em>20</em>, 1290, doi:<a href="https://doi.org/10.3390/ijms20061290">10.3390/ijms20061290</a>.</p> <p> </p> <p>- <strong>Annotations-***.csv : </strong>Tables containing ground-truth category classes (normal vs cystic) for the images in the zip file.</p> <p>The tables contain columns with the image filename, folder and category.</p> <p>Note : <strong>the Folder column should be updated with the root folder directory once downloaded on your machine.</strong></p> <p>These files were generated with the Fiji plugin <em>single-class (button)</em> from the <em>Qualitative-Annotations</em> update site.</p> <p>The 2 files contain the same information, they only differ in the formatting of the category, the <em>singleColumn </em>file has a single category column while the <em>multiColumn</em> has 2 columns (normal/cystic) with 0/1 encoding.</p> <p>The choice of category encoding solely depends on how the table is used, i.e. in which training workflow, home-made script or software.</p> <p>- <strong>trainedModel.zip : </strong>This archive contains 2 files: <strong>(1) </strong>a h5 file corresponding to a trained deep-learning model to classify the images of the dataset in the 2 categories (normal vs cystic), and <strong>(2)</strong> a text file containing the class names. Both files are necessary to predict the category of new images similar to the one in the dataset, for instance using the published KNIME workflows.</p>
Systemic Treatment with Cigarette Smoke Extract Affects Zebrafish Visual Behaviour, Intraocular Vasculature Morphology and Outer Segment Phagocytosis
<p>Underlying dataset and analysis tests of the results described in the article "Systemic Treatment with Cigarette Smoke Extract Affects Zebrafish Visual Behaviour, Intraocular Vasculature Morphology and Outer Segment Phagocytosis".</p>
zebrafish scRNA data set objects
<p>Combined and converted scRNA data from http://tome.gs.washington.edu/ (Qiu et al. 2022), see a detailed description of the study here: https://www.nature.com/articles/s41588-022-01018-x</p> <p>Data were downloaded from http://tome.gs.washington.edu/ as R rds files, combined into a single Seurat object and converted into loom and AnnData (h5ad) files to be able to analyse with e.g. python scanpy package.</p> <p>If you use this data, please cite Farrel et al. 2018, Wagner et al. 2018 and Qiu et al. 2022.</p>
data for Collective departures and leadership in zebrafish
<p>Txt files with the position (x,y) and confidence probability of the correct identification of the fish. Dataset used for the publication Collective departures and leadership in zebrafish.</p>
The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis
<p>This dataset contains zebrafish (<em>Danio rerio</em>) raw RNA and ChIP (paired-end) sequencing data:</p> <ul> <li>NDC-TLF-3dpf-repl*: 5 biological replicates of RNA-seq data from 3dpf wild-type (TL background) whole embryo lysates</li> <li>TLF-3dpf-replicate*: 3 biological replicates of RNA-seq data from 3dpf wild-type (TL background) whole embryo lysates</li> <li>WT[12]-3dpf-ChIP-H3K27me3*: 2 biological replicates of H3K27me3 ChIP-seq data from 3dpf wild-type (TU/TF mixed background) whole embryo lysates</li> <li>WT[12]-3dpf-H3K27me3-spikein*: 2 biological replicates of H3K27me3 ChIP-seq data (with Drosophila H2Ay spike in) from 3dpf wild-type (TU/TF mixed background) whole embryo lysates</li> <li>WT[12]-3dpf-Rnf2-spikein*: 2 biological replicates of Rnf2 ChIP-seq data (with Drosophila H2Ay spike in) from 3dpf wild-type (TU/TF mixed background) whole embryo lysates</li> <li>WT2-3dpf-input-spikein*: input ChIP-seq data (with Drosophila H2Ay spike in) from 3dpf wild-type (TU/TF mixed background) whole embryo lysates</li> </ul>
Gene-level counts according to their poly(A) length and additional uridine modifications in several stages of zebrafish, Xenopus, and mouse embryos
<p>This HDF5 file contains the processed data of primary poly(A) tail length analyses for the TAIL-seq runs used for Chang and Yeo et al. (2018; doi:10.1016/j.molcel.2018.03.004). The read count tables are stored under the two-level group structure of the run identifier as the first level and the sample identifier as the second level. A dataset at a leaf node is an unsigned integer array of the read count numbers by the length of poly(A) in rows and the length of U tails following after poly(A) in columns.</p> <p>Please refer to the <a href="https://data.mendeley.com/datasets/tzc5wwczyg/1">supplementary data page</a> of the original paper for more information about the experimental design.</p> <p> </p>
xrcc1 crispant zebrafish structural brain imaging
<p>Triple transgenic (vGlut2a:GFP, gad1b:RFP, tuba:mCar) 6 dpf larval zebrafish heads, scanned on confocal microscopy at 2x2x2 micron resolution. Files ending -01.nii.gz are vGlut2a:GFP channel, -02.nii.gz are tuba:mCar channel and -03.nii.gz are gad1b:RFP channel. </p> <p>xrcc1-t12.zip: xrcc1 tracr injected controls (ctr) and gRNA t1/2 crispants (inj)</p> <p>xrcc1-t56.zip: xrcc1 tracr injected controls (ctr) and gRNA t5/6 crispants (inj)</p> <p>xrcc1-parp1.zip: contains vGlut2a:GFP only. tracr injected controls (ctr), gRNA t1/2 xrcc1 crispants (xrc) and double gRNA t1/2 xrcc1 + gRNA t6/8 parp1 crispants (dbl).</p> <p> </p>
Dataset: Effect of decynium-22 on zebrafish anxiety-like behavior
<p>Data for the research project "Effect of decynium-22 on zebrafish anxiety-like behavior", collected at Laboratório de Neurociências e Comportamento "Frederico Guilherme Graeff", Faculdade de Psicologia, Universidade Federal do Sul e Sudeste do Pará.</p>
Genetic and epigenetic regulation of zebrafish intestinal development
<p>This dataset contains zebrafish (<em>Danio rerio</em>) raw RNA and ChIP (paired-end) sequencing data:</p> <ul> <li>RNA-seq <ul> <li>lane1_BSwt5dpf*: 3 biological replicates of RNA-seq data from 5dpf wild-type (AB background) pooled intestines</li> <li>lane1_BSwt7dpf*: 3 biological replicates of RNA-seq data from 7dpf wild-type (AB background) pooled intestines</li> <li>lane1_BSwt9dpf*: 3 biological replicates of RNA-seq data from 9dpf wild-type (AB background) pooled intestines</li> </ul> </li> <li>ChIP-seq <ul> <li>Cldn-wt-int-5dpf-H3K27me3*: 2 biological replicates of H3K27me3 ChIP-seq data from 5dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-5dpf-H3K4me3*: 2 biological replicates of H3K4me3 ChIP-seq data from 5dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-5dpf-input-12727_R[12].fastq.gz: 1 sample of input ChIP-seq data from 5dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-7dpf-H3K27me3*: 2 biological replicates of H3K27me3 ChIP-seq data from 7dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-7dpf-H3K4me3*: 2 biological replicates of H3K4me3 ChIP-seq data from 7dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-7dpf-input-12727_R[12].fastq.gz: 1 sample of input ChIP-seq data from 7dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-9dpf-H3K27me3*: 2 biological replicates of H3K27me3 ChIP-seq data from 9dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-9dpf-H3K4me3*: 2 biological replicates of H3K4me3 ChIP-seq data from 9dpf wild-type (AB background) pooled intestines</li> <li>Cldn-wt-int-9dpf-input-12727_R[12].fastq.gz: 1 sample of input ChIP-seq data from 9dpf wild-type (AB background) pooled intestines</li> </ul> </li> </ul>
Data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos
<p>This contains the data for the manuscript Feugere et al., "Heat induces multiomic and phenotypic stress propagation in zebrafish embryos" (2023). Zebrafish embryos were exposed to thermal stress ("TS") and stress metabolites ("SM") released by heat-stressed conspecifics in a two-way factorial design ("TSxSM"). The folder includes raw molecular data (cortisol levels, HSP70 protein levels, and gene expression acquired with LAMP and RNA-seq) and raw phenotypic data (morphology, hatching, survival, and behaviour) of zebrafish <em>Danio rerio </em>at 1 day and 4 days of development.</p> <p>The .csv files contain all quantitative data, whilst the .tab files contain the gene count data required for gene expression analysis. The data were analysed in R using the code shared in the "TSxSM2.stats.Rmd" file. The "Metadata" document provides the reader with an extensive description of each file.</p>
zebrafish GSE223922 scRNA data set objects
<p>scRNA data from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE223922 (Sur et al. 2023), see a detailed description of the study here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10055256/</p> <p>Data were downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE223922 to create a R Seurat object and converted into AnnData (h5ad) file to be able to analyse with e.g. python scanpy package.</p> <p>If you use this data, please cite Sur et al. 2023.</p>
Heatmaps of quantitative and qualitative phenotypes of zebrafish pronephroi upon compound exposure
<p>Heatmaps of quantitative and qualitative phenotypes of embryonic zebrafish pronephroi after exposure to compounds from the Prestwick library.</p> <p>For further details please see:</p> <p><em>Westhoff JH, Steenbergen PJ, Thomas LSV, Heigwer J, Bruckner T, Cooper L, Tönshoff B, Hoffmann GF and Gehrig J (2020) In vivo High-Content Screening in Zebrafish for Developmental Nephrotoxicity of Approved Drugs. Front. Cell Dev. Biol. 8:583. doi: 10.3389/fcell.2020.00583</em></p> <p>The images represent full resolution versions of the thumbnails presented in: </p> <ol> <li>Supplementary Figure 3 | Fully annotated heat map of quantitative features.</li> <li>Supplementary Figure 4 | Fully annotated heat map of qualitative features.</li> </ol> <p> </p> <p> </p>
Paternal effects in a wild-type zebrafish implicate a role of sperm-derived small RNAs
<p>While the importance of maternal effects has long been appreciated, a growing body of evidence now points to the paternal environment having an important influence on offspring phenotype. Indeed, research on rodent models suggests that paternal stress leaves an imprint on the behaviour and physiology of offspring via non-genetic information carried in the spermatozoa, however fish have been understudied with regard to these sperm-mediated effects. Here we investigated whether the zebrafish was subject to heritable influences of paternal stress by exposing males to stressors (conspecific-derived alarm cue, chasing, and bright light) before mating and assessing the behavioural and endocrine responses of their offspring, including their behavioural response to conspecific-derived alarm cue. We found that after males are exposed to stress, their larval offspring show weakened responses to stressors. Small RNA sequencing subsequently revealed that the levels of several small noncoding RNAs, including microRNAs, PIWI-interacting RNAs, and tRNA-derived small RNAs, were altered in the spermatozoa of stressed fathers, suggesting that stress-induced alterations to the spermatozoal RNA landscape may contribute to shaping offspring phenotype. The work demonstrates that paternal stress should not be overlooked as a source of phenotypic variation and that spermatozoal small RNAs may be important intergenerational messengers in fish.</p>
diatomsRcool/zebrafish_phenotype_survey: v1.0.0 Zebrafish Phenotype Survey
<p>No description provided.</p>
Srrm4 expression during neural development in zebrafish
<p>Confocal microscope z-stacks recording expression of srrm4 during neural development in zebrafish, ascertained using hybridization chain reaction (HCR) in situ hybridization against srrm4 together with additional genes as indicated in file titles. In each file, srrm4 is in channel 1 (green), and if a second gene is listed, its expression is in channel 2 (red). Ages are indicated in file names: hpf = hours post fertilization ; dpf = days post fertilization.</p> <p>srrm4_elavl3_avg_3dpf.tif : mean of three co-registered images.</p> <p>srrm4_elavl3_avg_5dpf.tif : mean of five co-registered images.</p>
Transcriptomic profiling of clobetasol propionate-induced immunosuppression in challenged zebrafish embryos
<p>We have conducted an immune challenge experiment on 48h zebrafish embryos, which were previously treated with the immunosuppressive drug clobetasol propionate (CP). The embryos' immune system was challenged by injection of a mix of different pathogen associated molecular patterns (PAMPs). RNA sequencing was performed in order to detect altered molcular expression levels induced by CP, PAMPs and a combination of both. The data was published in <a href="https://doi.org/10.1016/j.ecoenv.2022.113346" target="_blank" rel="noopener">Essfeld <em>et al.</em> 2022</a>.</p> <p>The uploaded data archive (<a href="https://www.7-zip.org/">7-zip</a> compressed) consists of three major data types:<br>1. MultiQC reports from raw RNA-Seq read processing and QC (50bp SR)<br>2. Result tables from differential gene expression analysis (DGEA) with DESEq2<br>3. Result tables from Overrespresentation Analysis (ORA) with clusterProfiler</p> <p>Gene count normalization and DGEA was conducted with DESeq2 (<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8">Love et al., 2014</a>, DOI 10.1186/s13059-014-0550-8) . Three biological replicates per condition, exposure treatments were compared with respect to the control group in a pairwise fashion, applying Wald’s t-test. P values were corrected for multiple testing with independent hypothesis weighting (IHW) (<a href="https://www.nature.com/articles/nmeth.3885">Ignatiadis et al., 2016</a>, DOI 10.1038/nmeth.3885 ) after Benjamini-Hochberg (BH). To improve the signal to statistical noise ratio, the obtained log<sub>2</sub>-fold change (lfc) values were shrunk with the apeglm method described by Zhu and colleagues (<a href="https://academic.oup.com/bioinformatics/article/35/12/2084/5159452?login=true">2019</a>, DOI 10.1093/bioinformatics/bty895 ) before DGEA result tables were subjected to ORA via clusterProfiler (<a href="https://www.liebertpub.com/doi/10.1089/omi.2011.0118">Yu et al., 2012</a>, DOI 10.1089/omi.2011.0118).</p> <p>The ArrayExpress accession number E-MTAB-11092, provides access to the raw and DESeq2 normalized gene count matrices upon which these analysis were performed. Genes were annotated through the biomaRt package (<a href="https://www.nature.com/articles/nprot.2009.97.pdf?origin=ppub">Durinck et al., 2009</a>, DOI 10.1038/nprot.2009.97 ) in R (<a href="https://www.r-project.org/">R Core Team 2021</a>).</p>
Shedding Light on Metal-Based Nanoparticles in Zebrafish by Computed Tomography with Micrometer Resolution
<p>Supplementary 3D image stacks of microtomography data.</p> <p>100 layer xy, xz, and yz image stacks</p> <p>Publication included as PDF file (open access, DOI: 10.1002/smll.202000746)</p> <p>********************************************</p> <p>Metal-based nanoparticles are clinically used for diagnostic and therapeutic<br> applications. After parenteral administration, they will distribute throughout<br> different organs. Quantification of their distribution within tissues in the 3D<br> space, however, remains a challenge owing to the small particle diameter.<br> In this study, synchrotron radiation-based hard X-ray tomography (SRμCT)<br> in absorption and phase contrast modes is evaluated for the localization of<br> superparamagnetic iron oxide nanoparticles (SPIONs) in soft tissues based<br> on their electron density and X-ray attenuation. Biodistribution of SPIONs<br> is studied using zebrafish embryos as a vertebrate screening model. This<br> label-free approach gives rise to an isotropic, 3D, direct space visualization<br> of the entire 2.5 mm-long animal with a spatial resolution of around 2<br> μm. High resolution image stacks are available on a dedicated internet<br> page (http://zebrafish.pharma-te.ch). X-ray tomography is combined with<br> physico-chemical characterization and cellular uptake studies to confirm the<br> safety and effectiveness of protective SPION coatings. It is demonstrated<br> that SRμCT provides unprecedented insights into the zebrafish embryo<br> anatomy and tissue distribution of label-free metal oxide nanoparticles.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.